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Vignettes #15

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4 of 5 tasks
TomSmithCGAT opened this issue Jan 11, 2021 · 3 comments
Open
4 of 5 tasks

Vignettes #15

TomSmithCGAT opened this issue Jan 11, 2021 · 3 comments

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@TomSmithCGAT
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TomSmithCGAT commented Jan 11, 2021 •
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  • Fasta files: preparing cRAP and reference proteomes
  • GO: Using goseq and simplifying results
  • SILAC
  • LFQ OOPS RNase +/-
  • Improve TMT (less notch, sum aggregation)
@TomSmithCGAT
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@csdaw - Starting writing a SILAC vignette. Would you mind updating the psm_silac_p4 and pep_silac_p4 objects so they have a greater intersection. As it stands, they only share 8 sequences, which makes them less than ideal for demonstrating estimate_incorporation(). I guess the easiest thing to do is to just create them in the same script so you can use the same sample of 100 proteins. I'd update myself, but I don't think I have access to the raw data. Happy to do so if you can share though

csdaw added a commit that referenced this issue Feb 2, 2022
@csdaw
Make silac_p4 objs intersect better
4392f0e 
See comment in #15
@csdaw
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csdaw commented Feb 2, 2022

@TomSmithCGAT done! This should help.

@TomSmithCGAT
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Brilliant. Thank you! Draft SILAC vignette isn't far off...

TomSmithCGAT added a commit that referenced this issue Feb 24, 2022
@TomSmithCGAT @csdaw
Ts add vignettes (#37)
7fee9d2 
* avoids error in remove_redundant_go when GO term has no ontology

* Fix message type in get_enriched_go()

* Add dataset from DEP package

Results of a differential enrichment analysis on
LFQ data which is provided in the DEP package.

Will be used for testing GO functions amongst
other things.

* Check input data type

get_enriched_go()

* minor updates to TMT vignette

* adds data for SILAC vignette and starts vignette

* adds futher steps to SILAC vignette

* Updates TMT vignette to clarify when notch section can be skipped

* Contiunes SILAC vignette

* Make silac_p4 objs intersect better

See comment in #15

* Getting close to first draft for SILAC vignette

* Finalises first draft of SILAC vignette

* adds DEqMS to suggests

* adds DEqMS to suggests (2)

* Many small changes to code + text

Mostly formatting and increasing consistency
with variable naming and function choice.

* Several changes to body text

* Change SILAC vignette title

* Add a section title

Co-authored-by: Charlotte Dawson <csdaw@outlook.com>
Co-authored-by: TomSmithCGAT <tss38@mrc-tox.cam.ac.uk>
@TomSmithCGAT TomSmithCGAT mentioned this issue Mar 9, 2022
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@TomSmithCGAT @csdaw